coefplot             package:pls             R Documentation(latin1)

_P_l_o_t _R_e_g_r_e_s_s_i_o_n _C_o_e_f_f_i_c_i_e_n_t_s _o_f _P_L_S_R _a_n_d _P_C_R _m_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Function to plot the regression coefficients of an 'mvr' object.

_U_s_a_g_e:

     coefplot(object, ncomp = object$ncomp, comps, intercept = FALSE,
              separate = FALSE, nCols, nRows, labels, type = "l",
              lty = 1:nLines, lwd = NULL, pch = 1:nLines, cex = NULL,
              col = 1:nLines, legendpos, xlab = "variable",
              ylab = "regression coefficient", main, pretty.xlabels = TRUE,
              xlim, ...)

_A_r_g_u_m_e_n_t_s:

  object: an 'mvr' object.  The fitted model.

ncomp, comps: vector of positive integers.  The components to plot. 
          See 'coef.mvr' for details.

separate: logical.  If 'TRUE', coefficients for different model sizes
          are blotted in separate plots.

intercept: logical.  Whether coefficients for the intercept should be
          plotted.  Ignored if 'comps' is specified.  Defaults to
          'FALSE'.  See 'coef.mvr' for details.

nCols, nRows: integer.  The number of coloumns and rows the plots will
          be laid out in.  If not specified, 'coefplot' tries to be
          intelligent.

  labels: optional.  Alternative x axis labels.  See Details.

    type: character.  What type of plot to make.  Defaults to '"l"'
          (lines).  Alternative types include '"p"' (points) and '"b"'
          (both).  See 'plot' for a complete list of types.

     lty: vector of line types (recycled as neccessary).  Line types
          can be specified as integers or character strings (see 'par'
          for the details).

     lwd: vector of positive numbers (recycled as neccessary), giving
          the width of the lines.

     pch: plot character.  A character string or a vector of single
          characters or integers (recycled as neccessary).  See
          'points' for all alternatives.

     cex: numeric vector of character expansion sizes (recycled as
          neccessary) for the plotted symbols.

     col: character or integer vector of colors for plotted lines and
          symbols (recycled as neccessary).  See 'par' for the details.

legendpos: Legend position.  Optional.  Ignored if 'separate' is
          'TRUE'.  If present, a legend is drawn at the given position.
          The position can be specified symbolically (e.g., 'legendpos
          = "topright"').  This requires R >= 2.1.0.  Alternatively,
          the position can be specified explicitly ('legendpos =
          t(c(x,y))') or interactively ('legendpos = locator()').  This
          only works well for plots of single-response models.

xlab,ylab: titles for x and y axes.  Typically character strings, but
          can be expressions (e.g., 'expression(R^2)' or lists.  See
          'title' for details.

    main: optional main title for the plot.  See Details.

pretty.xlabels: logical.  If 'TRUE', 'coefplot' tries to plot the x
          labels more nicely.  See Details.

    xlim: optional vector of length two, with the x limits of the plot.

     ...: Further arguments sent to the underlying plot functions.

_D_e_t_a_i_l_s:

     'coefplot' handles multiple responses by making one plot for each
     response.  If 'separate' is 'TRUE', separate plots are made for
     each combination of model size and response.  The plots are laid
     out in a rectangular fashion.

     If 'legendpos' is given, a legend is drawn at the given position
     (unless 'separate' is 'TRUE').

     The argument 'labels' can be a vector of labels or one of
     '"names"' and '"numbers"'.  The labels are used as x axis labels. 
     If 'labels' is '"names"' or '"numbers"', the variable names are
     used as labels, the difference being that with '"numbers"', the
     variable names are converted to numbers, if possible.  Variable
     names of the forms '"number"' or '"number text"' (where the space
     is optional), are handled.

     The argument 'main' can be used to specify the main title of the
     plot.  It is handled in a non-standard way.  If there is only on
     (sub) plot, 'main' will be used as the main title of the plot.  If
     there is _more_ than one (sub) plot, however, the presence of
     'main' will produce a corresponding 'global' title on the page. 
     Any graphical parametres, e.g., 'cex.main', supplied to 'coefplot'
     will only affect the 'ordinary' plot titles, not the 'global' one.
      Its appearance can be changed by setting the parameters with
     'par', which will affect _both_ titles.  (To have different
     settings for the two titles, one can override the 'par' settings
     with arguments to 'coefplot'.)

     The argument 'pretty.xlabels' is only used when 'labels' is
     specified.  If 'TRUE' (default), the code tries to use a 'pretty'
     selection of labels.  If 'labels' is '"numbers"', it also uses the
     numerical values of the labels for horisontal spacing.  If one has
     excluded parts of the spectral region, one might therefore want to
     use 'pretty.xlabels = FALSE'.

     The function can also be called through the 'mvr' plot method by
     specifying 'plottype = "coefficients"'.

_N_o_t_e:

     'legend' has many options.  If you want greater control over the
     appearance of the legend, omit the 'legendpos' argument and call
     'legend' manually.

     The handling of 'labels' and 'pretty.xlabels' is experimental.

_A_u_t_h_o_r(_s):

     Ron Wehrens and Bjrn-Helge Mevik

_S_e_e _A_l_s_o:

     'mvr', 'plot.mvr', 'coef.mvr', 'plot', 'legend'

_E_x_a_m_p_l_e_s:

     data(yarn)
     mod.nir <- plsr(density ~ NIR, ncomp = 8, data = yarn)
     ## Not run: 
     coefplot(mod.nir, ncomp = 1:6)
     plot(mod.nir, plottype = "coefficients", ncomp = 1:6) # Equivalent to the previous
     ## Plot with legend:
     coefplot(mod.nir, ncom = 1:6, legendpos = "bottomright")
     ## End(Not run)

     data(oliveoil)
     mod.sens <- plsr(sensory ~ chemical, ncomp = 4, data = oliveoil)
     ## Not run: coefplot(mod.sens, ncomp = 2:4, separate = TRUE)

